For first installation, and for any later upgrade, at code root location:
php cli/pfm-cli.php install
This will setup database i.e create tables, migrate/update schemas etc..
To know current version:
php cli/pfm-cli.php version --db
To add an upgrade (not an install from scratch) script:
php cli/pfm-cli.php upgrade --desc "fix this for that"
this will create a unique script in db/upgrade with a timestamp prefix.
You can then edit script to add whatever is needed for upgrade.
At install script will look for all scripts in db/upgrade (sorted by timestamp), and apply them one by one (and record its id in db).
If script has already been applied, it is skipped.